chore: remove pip packaged code #50
Workflow file for this run
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| name: Dry run dmux & lint Snakefile | |
| on: | |
| push: | |
| jobs: | |
| dry_run_and_lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://snakemake/snakemake:stable | |
| - name: Dry Run with test data | |
| run: | | |
| docker run -h cn0000 -v $PWD:/opt2 snakemake/snakemake:stable /bin/bash -c \ | |
| "pip install /opt2; dmux run -s /opt2/.tests/illumnia_demux -o /opt2/.tests/illumnia_demux/dry_run_out --local --dry-run /opt2/.tests/illumnia_demux" | |
| - name: View the pipeline config file | |
| run: | | |
| echo "Generated config file for pipeline...." && cat $PWD/.tests/illumnia_demux/dry_run_out/EXP_PROJ_demux/.config/config_job_0.json | |
| - name: Lint Snakefile | |
| continue-on-error: true | |
| run: | | |
| docker run -e SNK_CONFIG='/opt2/.tests/illumnia_demux/dry_run_out/.config/config_job_0.json' -v $PWD:/opt2 snakemake/snakemake:stable snakemake --lint -s /opt2/workflow/illumina/Snakefile -d /opt2/workflow/illumina || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' |